Entropy Balance in the Intercalation Process of an Anti-Cancer Drug Daunomycin

Abstract

I ntercalation 1 is one of the important biophysical processes by which anticancer drugs (such as daunomycin) interact with DNA causing subsequent death of cancerous cells. The enormous therapeutic significance of daunomycin 2 (DM) and related anticancer drugs 3 invoked exhaustive studies on thermodynamic analysis of the intercalation 4À6 and other drugÀDNA binding processes 7,8 portraying a general enthalpy/entropy balance. 9À11 Chaires surmised an interesting aspect of thermodynamic features of drugÀDNA binding from existing experimental observations that intercalation is primarily enthalpy driven, whereas minor groove-binding is entropy driven. 12 For DM intercalation, overall entropy change is small, À1.1 kcal/mol. 12,13 However, identifying molecular contributions to this overall small entropy change is beyond the scope of experiment. The aim of this Letter therefore is to capture entropy contributions of the individual components involved along the intercalation process to probe into the molecular aspects of the thermodynamics of the process, in particular, and recognition processes, in general. This essentially boils down to the calculation of the DM, DNA and water entropy in the different stages along the intercalation process, as adopted in the study providing the first account of such entropy decomposition (including water) in a molecular recognition process.Thermodynamic aspects (enthalpy, entropy) of the overall intercalation process have been studied extensively using experimental techniques 4À6 and computational methods using continuum solvent, 14,15 ab initio quantum calculation, 16 and statistical mechanical approach. 17 However, contributions of various entropic components for intercalation or other molecular recognition processes have not been addressed.Entropy calculation using computational methods is extremely challenging. Only recently, an upsurge of such entropy calculations in various biological systems 18À25 is observed. The most common method to estimate biomolecular entropy is quasi-harmonic (QH) approximation. 26À28 Although it is effective, it suffers from two caveats; it requires long simulations to converge 19 and provides the upper limit of configurational entropy, which often overestimates true entropy. 29 Therefore, various corrections have been proposed 19,30À32 to obtain accurate estimate involving anharmonic and mutual information corrections. Water entropy, however, cannot directly be estimated using QH method because of its diffusive nature. Only recently, Grubmuller and coworkers have proposed a permutation reduction (PR) method to reduce the configurational volume of water by factorial N, thereby allowing the use of QH method for entropy calculation, 33 which has found application in structural changes of DNA and RNA. 18 Another method of calculating water entropy, proposed previously by Goddard and coworkers, 34 has been applied in DNA grooves 35 and bilayer. 36 Entropy change also originates from the loss of rotational and translational degrees of freedom (ΔS t+r ). Ho...

Metal complex interactions with DNA

“…93,94 This effect however is dependent upon the "depth of insertion". [98][99][100] Common organic intercalators include phenanthrolines, 101 phenanthridines, 102 acridines, 102 anthraquinones, 103 anthracenes, 104 and ellipticines. [98][99][100] Common organic intercalators include phenanthrolines, 101 phenanthridines, 102 acridines, 102 anthraquinones, 103 anthracenes, 104 and ellipticines.…”

Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins

“…The pRDF method has been used for calculating solvation entropy changes during the intercalation process of an anticancer drug. 20 …”

Role of Mg2+ ions in flavin recognition by RNA aptamer

“…A negative change in entropy can be attributed to the favorable electrostatic interactions between ligands and RNA [55,57]. Note that the resultant entropy change appeared during flavins-aptamer binding is the combined effect of drug entropy change, RNA entropy change as well as entropy change of water during binding process [58]. It is obvious that drug entropy will decrease while binds to aptamer, and the flexibility of RNA decreases during the interaction with drug or protein [59].…”

“…It is obvious that drug entropy will decrease while binds to aptamer, and the flexibility of RNA decreases during the interaction with drug or protein [59]. On the other hand, water entropy generally increases when a drug binds to DNA/RNA, as water molecules are coming out from the surrounding of ligand binding location in RNA [58]. Therefore, the negative entropy is originated by the cancellation of positive entropy change for water by the negative entropy change of RNA as well as flavins.…”